# LEMMI container for kaiju
# It is based on the biobox idea, see bioboxes.org
# No validation using yaml files required here yet

FROM ubuntu:14.04

ENV PACKAGES make gcc wget libc6-dev zlib1g-dev ca-certificates xz-utils

RUN apt-get update --fix-missing -y && apt-get install -y --no-install-recommends ${PACKAGES}

RUN apt-get install --fix-missing python3 git build-essential -y

RUN yes | perl -MCPAN -e "CPAN::Shell->notest(qw!install  List::MoreUtils!)"

RUN yes | perl -MCPAN -e "CPAN::Shell->notest(qw!install  Parallel::ForkManager!)"

RUN git clone https://github.com/bioinformatics-centre/kaiju.git

WORKDIR /kaiju/src

RUN git checkout d8730c6fc1d808728f8c9dfece3ae621d79d1ea0

RUN make

ENV KAJ /kaiju

ENV PATH ${PATH}:${KAJ}

ADD entry /usr/local/bin/

ADD Taskfile /

ADD scripts/extract_taxid.sh /

ADD scripts/extract_taxid.py /

ADD scripts/prepare_fasta.py /

ADD scripts/prepare_inputs.sh /

ADD scripts/prepare_results.py /

WORKDIR /bbx/tmp

ENTRYPOINT ["entry"]
